[gmx-users] TIP4P water model

Ankita naithani ankitanaithani at gmail.com
Fri Sep 21 17:48:37 CEST 2012

Hi all,

I am trying to begin a simulation of a protein.

I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.

when  I issue the grompp command to generate the necessary .tpr file
for simulation to be utilised by genion tool, I get the following
error :

"Fatal error:
number of coordinates in coordinate file (system_solv.gro, 421880)
             does not match topology (topol.top, 416008)

However, I have rechecked several times my topology file and the
co-ordinate file and I am running it pretty straightforward to get
this error. When I try TIP3P water model for the same protein, I do
not get the error.

I get the same error when I use TIP4P-Ew water model too. I have
decide a better water model for my system before I run my final
production simulations and so I have been trying to compare both the
water models. I am wondering if anyone could kindly suggest the
possible reason for this error because ideally, it should not be
giving me any error at this stage as I haven't manipulated with

I am also appending my ions.mdp info below:

; ions.mdp - used as input into grompp to generate ions.tpr
; Parameters describing what to do, when to stop and what to save
integrator	= steep		; Algorithm (steep = steepest descent minimization)
emtol		= 1000.0  	; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep          = 0.01          ; Energy step size
nsteps		= 50000	  	; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist		= 1		; Frequency to update the neighbor list and long range forces
ns_type		= grid		; Method to determine neighbor list (simple, grid)
rlist		= 0.9		; Cut-off for making neighbor list (short range forces)
coulombtype	= PME		; Treatment of long range electrostatic interactions
rcoulomb	= 0.9		; Short-range electrostatic cut-off
rvdw		= 0.9		; Short-range Van der Waals cut-off
pbc		= xyz 		; Periodic Boundary Conditions (yes/no)


Ankita Naithani

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